Stored Procedures was included and supported by MySQL since v5.0 I think?
Anywho, I use stored procedures for e.g. myDBR and report generation from various web applications and for automation of reporting. I see this becomming more and more common nowdays.

This is one of the features I really miss in HeidiSQL along with tab'ed connections (multiple DB connections in one instance). A extended DBA module is also on my wishlist, make these 3 things come true and you will be the #1 choice of all DBdevs, DBAs etc. for MySQL!

I would recommend a quick view of a Quest Toad for Oracle trial to get some inspiration around tab'ed connections and/or triggers/stored procedures. They did a great job with their Oracle client. Copy with pride :)